Figure 1

A diagrammatic representation of transcript prediction using ALTSCAN and validation pipeline based on RNA-seq datasets.

The upper part shows the pipeline of alternative transcript prediction and the MIXTURE dataset construction. The lower part shows the pipeline for transcript validation with RNA-seq data. The grey blocks indicate raw public data. Candidate gene regions were extracted from various public annotations and then ASs were predicted by ALTSCAN for these regions. Together with the well-annotated KNOWN transcripts, ALTSCAN transcripts were validated with a large number of RNA-seq data. TC is short for transcript coverage and JC is short for junction coverage. The NIJ (novel internal junction) filter was used to check if novel internal junction(s) existed in transcripts (Figure S3). The novel transcript datasets VHC, VMC and VLC were defined as in the figure.